# HG changeset patch
# User iuc
# Date 1595365481 14400
# Node ID 7a76cd412252d04cbafacf4ae86ebc96677ef278

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"

diff -r 000000000000 -r 7a76cd412252 data_manager/data_manager_ncbi_taxonomy_sqlite.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_ncbi_taxonomy_sqlite.py	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,79 @@
+from __future__ import division, print_function
+
+import argparse
+import datetime
+import json
+import os
+import os.path
+import shlex
+import subprocess
+
+DATA_TABLE_NAME = "ncbi_taxonomy_sqlite"
+
+
+def build_sqlite(taxonomy_dir, output_directory, name=None, description=None):
+    if not os.path.exists(output_directory):
+        os.mkdir(output_directory)
+    output_filename = os.path.join(output_directory, "tax.ncbitaxonomy.sqlite")
+    cmd_str = "taxonomy_util -d {} to_sqlite {}".format(output_filename, taxonomy_dir)
+    cmd = shlex.split(cmd_str)
+    subprocess.check_call(cmd)
+
+    today_str = datetime.date.today().strftime("%Y-%m-%d")
+    if name is None or name.strip() == "":
+        name = "ncbitaxonomy_build_" + today_str
+
+    if description is None or description.strip() == "":
+        description = "NCBI Taxonomy database (built on {})".format(today_str)
+
+    data = [dict(value=name, description=description, path=output_filename)]
+    return data
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Build SQLite database from NCBI taxonomy"
+    )
+    parser.add_argument(
+        "--output_directory", default="tmp", help="Directory to write output to"
+    )
+    parser.add_argument(
+        "taxonomy_dir",
+        help="Path to directory containing NCBI Taxonomy nodes.dml and names.dmp file"
+    )
+    parser.add_argument(
+        "name",
+        help="Name to use for the entry in the data table"
+    )
+    parser.add_argument(
+        "description",
+        help="Description to use for the entry in the data table"
+    )
+    parser.add_argument(
+        "galaxy_datamanager_filename",
+        help="Galaxy JSON format file describing data manager inputs",
+    )
+    args = parser.parse_args()
+
+    config = json.load(open(args.galaxy_datamanager_filename))
+    output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
+    if output_directory is None:
+        output_directory = args.output_directory
+
+    if not os.path.isdir(output_directory):
+        os.makedirs(output_directory)
+
+    data_manager_dict = {}
+    data_manager_dict["data_tables"] = json.load(
+        open(args.galaxy_datamanager_filename)
+    ).get("data_tables", {})
+    data_manager_dict["data_tables"] = data_manager_dict.get("data_tables", {})
+    data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[
+        "data_tables"
+    ].get(DATA_TABLE_NAME, [])
+
+    data = build_sqlite(args.taxonomy_dir, args.output_directory, args.name, args.description)
+
+    data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data)
+    print(json.dumps(data_manager_dict))
+    json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w"))
diff -r 000000000000 -r 7a76cd412252 data_manager/data_manager_ncbi_taxonomy_sqlite.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_ncbi_taxonomy_sqlite.xml	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,98 @@
+<tool id="data_manager_ncbi_taxonomy_sqlite" name="NCBI Taxonomy SQLite builder" tool_type="manage_data" profile="18.09" version="@PACKAGE_VERSION@+galaxy1" python_template_version="3.5">
+    <macros>
+        <token name="@PACKAGE_VERSION@">1.0.5</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@PACKAGE_VERSION@">rust-ncbitaxonomy</requirement>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $taxonomy.taxonomy_source == 'cached':
+            #set $taxonomy_dir = $taxonomy.taxonomy_table.fields.path
+        #else
+            mkdir taxonomy && ln -s '$taxonomy.nodes' taxonomy/nodes.dmp && ln -s '$taxonomy.names' taxonomy/names.dmp &&
+            #set $taxonomy_dir = 'taxonomy'
+        #end if 
+        python '$__tool_directory__/data_manager_ncbi_taxonomy_sqlite.py' '$taxonomy_dir' '$name' '$description' '$output_file'
+    ]]></command>
+    <inputs>
+        <conditional name="taxonomy">
+            <param name="taxonomy_source" type="select" label="Choose source of NCBI Taxonomy">
+                <option value="cached" selected="true">Use built-in NCBI Taxonomy database</option>
+                <option value="history">Datasets from history</option>
+            </param>
+            <when value="cached">
+                <param type="select" name="taxonomy_table" label="NCBI Taxonomy database">
+                    <options from_data_table="ncbi_taxonomy">
+                        <filter type="sort_by" column="1" /> 
+                        <validator type="no_options" message="No NCBI Taxonomy downloads are available" />
+                    </options>
+                    <validator type="no_options" message="No NCBI Taxonomy database download is available" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="nodes" type="data" format="txt" label="NCBI Taxonomy nodes.dmp file" />
+                <param name="names" type="data" format="txt" label="NCBI Taxonomy names.dmp file" />
+            </when>
+        </conditional>
+        <param name="name" type="text" label="Name of taxonomy database" help="(leave blank to use name based on today's date)" />
+        <param name="description" type="text" label="Description of taxonomy database" help="(leave blank to use name based on today's date)" />
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/> 
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="taxonomy">
+                <param name="taxonomy_source" value="history" />
+                <param name="nodes" ftype="txt" value="taxdb/nodes.dmp" />
+                <param name="names" ftype="txt" value="taxdb/names.dmp" />
+            </conditional>
+            <param name="name" value="test" />
+            <param name="description" value="test database" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="tax.ncbitaxonomy.sqlite" />
+                    <has_text text="test database" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <conditional name="taxonomy">
+                <param name="taxonomy_source" value="cached" />
+                <param name="taxonomy_table" value="sample" />
+            </conditional>
+            <param name="name" value="test" />
+            <param name="description" value="test database" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="tax.ncbitaxonomy.sqlite" />
+                    <has_text text="test database" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        The data manager creates a SQLite version the NCBI Taxonomy database, using the plain text files of the
+        NCBI database as input. Storing the database as a SQLite database allows for faster querying.
+
+        Input is either from the individual files (nodes.dmp and names.dmp) from the NCBI Taxonomy database or
+        from a previously downloaded code of the database stored as "reference data" in the Galaxy server.
+
+        .. class: infomark
+
+        *Notice:** If you leave name, or description blank, it will be generated automatically from the current date.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">@misc{vanHeusen2020,
+        author = {van Heusden, P.},
+        title = {a Rust crate for working with a local copy of the NCBI Taxonomy database },
+        year = {2020},
+        publisher = {GitHub},
+        journal = {GitHub repository},
+        howpublished = {\url{https://github.com/pvanheus/ncbitaxonomy}},
+        commit = {84d79cdcf2adb262c61511f8c7b9eceb5299b87d}
+        }
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 7a76cd412252 data_manager_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/data_manager_ncbi_taxonomy_sqlite.xml" id="data_manager_ncbi_taxonomy_sqlite" version="0.0.1">
+        <data_table name="ncbi_taxonomy_sqlite">
+            <output>
+                <column name="value" />
+                <column name="description" />
+                <column name="path" output_ref="output_file">
+                    <move type="directory" relativize_symlinks="True">
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">ncbi_taxonomy_sqlite/${value}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/ncbi_taxonomy_sqlite/${value}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>
diff -r 000000000000 -r 7a76cd412252 test-data/ncbi_taxonomy.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ncbi_taxonomy.loc	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,2 @@
+#value	name		path
+sample	sample database	${__HERE__}/taxdb
diff -r 000000000000 -r 7a76cd412252 test-data/ncbi_taxonomy_sqlite.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ncbi_taxonomy_sqlite.loc	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,2 @@
+#value	description	path
+test	test database	/tmp/tmpVxsQba/tmpUjPjFN/tmpjKzenM/database/data_manager_tool-data9y_VHy/ncbi_taxonomy_sqlite/test
diff -r 000000000000 -r 7a76cd412252 test-data/ncbi_taxonomy_sqlite_data_manager.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ncbi_taxonomy_sqlite_data_manager.json	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,1 @@
+{"data_tables": {"ncbi_taxonomy_sqlite": [{"value": "test", "path": "tmp/tax.ncbitaxonomy.sqlite", "description": "test database"}]}
\ No newline at end of file
diff -r 000000000000 -r 7a76cd412252 test-data/taxdb/names.dmp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxdb/names.dmp	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,687 @@
+1	|	all	|		|	synonym	|
+1	|	root	|		|	scientific name	|
+10239	|	Vira	|		|	synonym	|
+10239	|	Viridae	|		|	synonym	|
+10239	|	Viruses	|		|	scientific name	|
+10239	|	viruses	|	viruses <blast10239>	|	blast name	|
+12333	|	bacterial virus	|	bacterial virus <unclassified bacterial viruses>	|	in-part	|
+12333	|	bacterial viruses	|	bacterial viruses <unclassified bacterial viruses>	|	in-part	|
+12333	|	prokaryotic virus	|	prokaryotic virus <unclassified bacterial viruses>	|	in-part	|
+12333	|	unclassified bacterial viruses	|		|	scientific name	|
+12333	|	unclassified bacteriophages	|		|	synonym	|
+12333	|	unclassified phage	|		|	synonym	|
+12333	|	unclassified phages	|		|	synonym	|
+12340	|	Bacteriophage 933J	|		|	synonym	|
+12340	|	Coliphage 933J	|		|	synonym	|
+12340	|	Enterobacteria phage 933J	|		|	scientific name	|
+12340	|	phage 933J	|		|	synonym	|
+12347	|	Actinophage JHJ-1	|		|	scientific name	|
+12347	|	Bacteriophage JHJ-1	|		|	synonym	|
+12366	|	Bacteriophage h4489a	|		|	synonym	|
+12366	|	Streptococcus pyogenes bacteriophage H4489A	|		|	synonym	|
+12366	|	Streptococcus pyogenes phage H4489A	|		|	scientific name	|
+12371	|	Bacteriophage h30	|		|	synonym	|
+12371	|	Phage h30	|		|	scientific name	|
+12374	|	Lactococcus bacteriophage	|		|	synonym	|
+12374	|	Lactococcus phage	|		|	scientific name	|
+12375	|	Lactococcus 1 bacteriophage	|		|	synonym	|
+12375	|	Lactococcus bacteriophage (ISOLATE 7-9)	|		|	synonym	|
+12375	|	Lactococcus phage (ISOLATE 7-9)	|		|	scientific name	|
+12386	|	Lactococcus phage mi7-9	|		|	scientific name	|
+12388	|	Mycobacterium phage FRAT1	|		|	scientific name	|
+12388	|	mycobacteriophage FRAT1	|		|	synonym	|
+12392	|	Bacteriophage mv4	|		|	synonym	|
+12392	|	Lactobacillus delbrueckii subsp. bulgaricus phage mv4	|		|	synonym	|
+12392	|	Lactobacillus phage mv4	|		|	scientific name	|
+12392	|	Lactococcus delbrueckii bacteriophage MV4	|		|	synonym	|
+12392	|	phage mv4	|		|	synonym	|
+12403	|	Bacteriophage P32	|		|	synonym	|
+12403	|	Leuconostoc oenos phage P32	|		|	synonym	|
+12403	|	Leuconostoc phage P32	|		|	scientific name	|
+12404	|	Bacteriophage P37	|		|	synonym	|
+12404	|	Leuconostoc oenos phage P37	|		|	synonym	|
+12404	|	Leuconostoc phage P37	|		|	scientific name	|
+12405	|	Bacteriophage P54	|		|	synonym	|
+12405	|	Leuconostoc oenos phage P54	|		|	synonym	|
+12405	|	Leuconostoc phage P54	|		|	scientific name	|
+12406	|	Bacteriophage PAt5-12	|		|	synonym	|
+12406	|	Leuconostoc oenos phage PAt5-12	|		|	synonym	|
+12406	|	Leuconostocphage PAt5-12	|		|	scientific name	|
+12408	|	Bacteriophage PZt11-15	|		|	synonym	|
+12408	|	Leuconostoc oenos phage PZt11-15	|		|	synonym	|
+12408	|	Leuconostoc phage PZt11-15	|		|	scientific name	|
+12409	|	Bacteriophage d-16 phi	|		|	synonym	|
+12409	|	Clostridium phage d-16 phi	|		|	scientific name	|
+12412	|	Staphylococcus aureus bacteriophage phi-42	|		|	synonym	|
+12412	|	Staphylococcus aureus phage phi-42	|		|	synonym	|
+12412	|	Staphylococcus phage phi-42	|		|	scientific name	|
+12412	|	bacteriophage phi 42	|		|	synonym	|
+12412	|	bacteriophage phi-42	|		|	synonym	|
+12413	|	Bacteriophage phi 7-9	|		|	synonym	|
+12413	|	Lactococcusphage phi7-9	|		|	scientific name	|
+12420	|	Filamentous bacteriophage	|		|	synonym	|
+12420	|	Filamentous phage	|		|	scientific name	|
+12424	|	Bacteriophage 13	|		|	synonym	|
+12424	|	Phage 13	|		|	scientific name	|
+12425	|	Bacteriophage 16	|		|	synonym	|
+12425	|	Phage 16	|		|	scientific name	|
+12427	|	Lactococcus lactis phage phi 197	|		|	scientific name	|
+12427	|	phage phi 197	|		|	synonym	|
+12427	|	phage phi-197	|		|	synonym	|
+12428	|	Retronphage phi R73	|		|	scientific name	|
+28368	|	Corynebacterium diphtheriae phage	|		|	scientific name	|
+28368	|	Corynebacterium diphtheriae virus	|		|	synonym	|
+31760	|	Colitis phage	|		|	scientific name	|
+33768	|	Bacteriophage L10	|		|	synonym	|
+33768	|	Leuconostoc oenos bacteriophage L10	|		|	synonym	|
+33768	|	Leuconostoc oenos phage L10	|		|	synonym	|
+33768	|	Leuconostoc phage L10	|		|	scientific name	|
+33769	|	Bacteriophage mv1	|		|	synonym	|
+33769	|	Lactobacillus delbrueckii bacteriophage mv1	|		|	synonym	|
+33769	|	Lactobacillus delbrueckii subsp. bulgaricus phage mv1	|		|	synonym	|
+33769	|	Lactobacillus phage mv1	|		|	scientific name	|
+38018	|	Bacteriophage sp.	|		|	synonym	|
+38018	|	bacteriophage	|		|	synonym	|
+38018	|	bacteriophages	|		|	synonym	|
+38018	|	unidentified bacteriophage	|		|	synonym	|
+38018	|	unidentified phage	|		|	scientific name	|
+39425	|	Bacteriophage T270	|		|	synonym	|
+39425	|	Streptococcus phage T270	|		|	scientific name	|
+39943	|	Actinophage JHJ-3	|		|	scientific name	|
+39943	|	Bacteriophage JHJ-3	|		|	synonym	|
+41669	|	Bacteriophage LM4	|		|	synonym	|
+41669	|	Phage LM4	|		|	scientific name	|
+42171	|	Bacteriophage N 209	|		|	synonym	|
+42171	|	Phage N 209	|		|	scientific name	|
+42172	|	Bacteriophage 3/14	|		|	synonym	|
+42172	|	Phage 3/14	|		|	scientific name	|
+42173	|	Bacteriophage Cz	|		|	synonym	|
+42173	|	Phage Cz	|		|	scientific name	|
+45331	|	Bacteriophage fuse 5	|		|	synonym	|
+45331	|	Phage fuse 5	|		|	scientific name	|
+45332	|	Bacteriophage phi AR29	|		|	synonym	|
+45332	|	Prevotella phage phi AR29	|		|	scientific name	|
+45441	|	Bacteriophage L	|		|	synonym	|
+45441	|	Enterobacteria phage L	|		|	scientific name	|
+48224	|	Bacteriophage E	|		|	synonym	|
+48224	|	Phage E	|		|	scientific name	|
+53480	|	Virus-like particle CAK1	|		|	scientific name	|
+54392	|	Leuconostoc oenos bacteriophage 10MC	|		|	synonym	|
+54392	|	Leuconostoc phage 10MC	|		|	scientific name	|
+54392	|	Oenococcus oeni bacteriophage 10MC	|		|	synonym	|
+57476	|	Bacillus cereus bacteriophage 12826	|		|	synonym	|
+57476	|	Bacillus phage 12826	|		|	scientific name	|
+57476	|	Bacteriophage 12826	|		|	synonym	|
+60457	|	Bartonella henselae phage 60457	|		|	scientific name	|
+63117	|	Vibrio cholerae V86 phage	|		|	scientific name	|
+65388	|	Mycobacteriophage Ms6	|		|	synonym	|
+65388	|	Mycobacterium phage Ms6	|		|	scientific name	|
+73492	|	Streptococcus pyogenes phage	|		|	scientific name	|
+76262	|	Bacteriophage phiU	|		|	synonym	|
+76262	|	Rhizobium phage phiU	|		|	scientific name	|
+77920	|	Bacteriophage #D	|		|	synonym	|
+77920	|	Phage #D	|		|	scientific name	|
+86065	|	Streptococcus pyogenes bacteriophage H10403	|		|	synonym	|
+86065	|	Streptococcus pyogenes phage H10403	|		|	scientific name	|
+89551	|	Corynephage phi16	|		|	scientific name	|
+100637	|	Lactococcus lactis bacteriophage Q42	|		|	synonym	|
+100637	|	Lactococcus phage Q42	|		|	scientific name	|
+100638	|	Lactococcus lactis bacteriophage Q44	|		|	synonym	|
+100638	|	Lactococcus phage Q44	|		|	scientific name	|
+100639	|	Lactococcus lactis bacteriophage Q7	|		|	synonym	|
+100639	|	Lactococcus phage Q7	|		|	scientific name	|
+100640	|	Lactococcus lactis bacteriophage eb1	|		|	synonym	|
+100640	|	Lactococcus phage eb1	|		|	scientific name	|
+105686	|	Lambdoid phage HB-4	|		|	scientific name	|
+108916	|	Bacteriophage F3	|		|	synonym	|
+108916	|	Enterobacteria phage F3	|		|	scientific name	|
+108917	|	Bacteriophage F5	|		|	synonym	|
+108917	|	Enterobacteria phage F5	|		|	scientific name	|
+108918	|	Bacteriophage F6	|		|	synonym	|
+108918	|	Enterobacteria phage F6	|		|	scientific name	|
+112596	|	Bacteriophage WO	|		|	synonym	|
+112596	|	Wolbachia phage WO	|		|	scientific name	|
+112596	|	phage WO	|		|	synonym	|
+126970	|	Clostridium limosum phage	|		|	scientific name	|
+128975	|	Phage Fels-1	|		|	synonym	|
+128975	|	Salmonella phage Fels-1	|		|	scientific name	|
+128975	|	bacteriophage Fels-1	|		|	synonym	|
+129861	|	Phage Gifsy-1	|		|	scientific name	|
+129861	|	Salmonella typhimurium phage Gifsy-1	|		|	synonym	|
+129862	|	Phage Gifsy-2	|		|	scientific name	|
+129862	|	Salmonella typhimurium phage Gifsy-2	|		|	synonym	|
+132905	|	Neisseria meningitidis phage 2120	|		|	scientific name	|
+137422	|	Bacteriophage P4282	|		|	synonym	|
+137422	|	Ralstonia phage P4282	|		|	scientific name	|
+147128	|	Bartonella henselae phage	|		|	scientific name	|
+148339	|	Bacteriophage GMSE-1	|		|	synonym	|
+148339	|	Phage GMSE-1	|		|	scientific name	|
+156614	|	environmental samples	|	environmental samples <bacteriophages>	|	scientific name	|
+156615	|	Cyanophage clone GS2601	|		|	scientific name	|
+156616	|	Cyanophage clone GS2602	|		|	scientific name	|
+156617	|	Cyanophage clone GS2603	|		|	scientific name	|
+156618	|	Cyanophage clone GS2607	|		|	scientific name	|
+156619	|	Cyanophage clone GS2608	|		|	scientific name	|
+156620	|	Cyanophage clone GS2614	|		|	scientific name	|
+156621	|	Cyanophage clone GS2620	|		|	scientific name	|
+156622	|	Cyanophage clone GS2624	|		|	scientific name	|
+156623	|	Cyanophage clone GS2626	|		|	scientific name	|
+156624	|	Cyanophage clone GS2633	|		|	scientific name	|
+156625	|	Cyanophage clone GS2649	|		|	scientific name	|
+156626	|	Cyanophage clone GS2650	|		|	scientific name	|
+156627	|	Cyanophage clone GS2651	|		|	scientific name	|
+156653	|	Cyanophage clone SE1	|		|	scientific name	|
+156654	|	Cyanophage clone SE2	|		|	scientific name	|
+156655	|	Cyanophage clone SE3	|		|	scientific name	|
+156656	|	Cyanophage clone SE4	|		|	scientific name	|
+156657	|	Cyanophage clone SE5	|		|	scientific name	|
+156658	|	Cyanophage clone SE6	|		|	scientific name	|
+156659	|	Cyanophage clone SE7	|		|	scientific name	|
+156660	|	Cyanophage clone SE8	|		|	scientific name	|
+156661	|	Cyanophage clone SE11	|		|	scientific name	|
+156662	|	Cyanophage clone SE12	|		|	scientific name	|
+156663	|	Cyanophage clone SE9	|		|	scientific name	|
+156664	|	Cyanophage clone SE13	|		|	scientific name	|
+156665	|	Cyanophage clone SE14	|		|	scientific name	|
+156666	|	Cyanophage clone SE15	|		|	scientific name	|
+156667	|	Cyanophage clone SE17	|		|	scientific name	|
+156668	|	Cyanophage clone SE18	|		|	scientific name	|
+156669	|	Cyanophage clone SE19	|		|	scientific name	|
+156670	|	Cyanophage clone SE21	|		|	scientific name	|
+156671	|	Cyanophage clone SE22	|		|	scientific name	|
+156672	|	Cyanophage clone SE24	|		|	scientific name	|
+156673	|	Cyanophage clone SE26	|		|	scientific name	|
+156674	|	Cyanophage clone SE27	|		|	scientific name	|
+156675	|	Cyanophage clone SE29	|		|	scientific name	|
+156676	|	Cyanophage clone SE31	|		|	scientific name	|
+156677	|	Cyanophage clone SE34	|		|	scientific name	|
+156678	|	Cyanophage clone SE36	|		|	scientific name	|
+156679	|	Cyanophage clone SE37	|		|	scientific name	|
+156680	|	Cyanophage clone SE38	|		|	scientific name	|
+156681	|	Cyanophage clone SE39	|		|	scientific name	|
+156711	|	Cyanophage clone GS2701	|		|	scientific name	|
+156712	|	Cyanophage clone GS2704	|		|	scientific name	|
+156713	|	Cyanophage clone GS2705	|		|	scientific name	|
+156714	|	Cyanophage clone GS2707	|		|	scientific name	|
+156715	|	Cyanophage clone GS2708	|		|	scientific name	|
+156716	|	Cyanophage clone GS2711	|		|	scientific name	|
+156717	|	Cyanophage clone GS2712	|		|	scientific name	|
+156718	|	Cyanophage clone GS2713	|		|	scientific name	|
+156719	|	Cyanophage clone GS2714	|		|	scientific name	|
+156720	|	Cyanophage clone GS2717	|		|	scientific name	|
+156721	|	Cyanophage clone GS2721	|		|	scientific name	|
+156722	|	Cyanophage clone GS2723	|		|	scientific name	|
+156723	|	Cyanophage clone GS2732	|		|	scientific name	|
+156724	|	Cyanophage clone GS2733	|		|	scientific name	|
+156725	|	Cyanophage clone GS2734	|		|	scientific name	|
+156726	|	Cyanophage clone GS2735	|		|	scientific name	|
+156727	|	Cyanophage clone GS2736	|		|	scientific name	|
+156728	|	Cyanophage clone GS2737	|		|	scientific name	|
+156729	|	Cyanophage clone GS2738	|		|	scientific name	|
+156730	|	Cyanophage clone GS2739	|		|	scientific name	|
+156731	|	Cyanophage clone GS2745	|		|	scientific name	|
+156732	|	Cyanophage clone GS2747	|		|	scientific name	|
+156733	|	Cyanophage clone GS2748	|		|	scientific name	|
+156740	|	Synechococcus phage 27A	|		|	scientific name	|
+156740	|	Synechococcus phage isolate 27A	|		|	synonym	|
+156741	|	Synechococcus phage 31B	|		|	scientific name	|
+156742	|	Synechococcus phage 32A	|		|	scientific name	|
+156743	|	Synechococcus phage 44A	|		|	scientific name	|
+156745	|	Synechococcus phage P6	|		|	scientific name	|
+156746	|	Synechococcus phage P12	|		|	scientific name	|
+156747	|	Synechococcus phage P17	|		|	scientific name	|
+156748	|	Synechococcus phage P77	|		|	scientific name	|
+156749	|	Synechococcus phage P79	|		|	scientific name	|
+156750	|	Synechococcus phage P81	|		|	scientific name	|
+156767	|	Cyanophage clone SS4016	|		|	scientific name	|
+156768	|	Cyanophage clone SS4017	|		|	scientific name	|
+156769	|	Cyanophage clone SS4018	|		|	scientific name	|
+156770	|	Cyanophage clone SS4019	|		|	scientific name	|
+156771	|	Cyanophage clone SS4020	|		|	scientific name	|
+156772	|	Cyanophage clone SS4021	|		|	scientific name	|
+156773	|	Cyanophage clone SS4026	|		|	scientific name	|
+156774	|	Cyanophage clone SS4027	|		|	scientific name	|
+156775	|	Cyanophage clone SS4028	|		|	scientific name	|
+156776	|	Cyanophage clone SS4029	|		|	scientific name	|
+156777	|	Cyanophage clone SS4033	|		|	scientific name	|
+156778	|	Cyanophage clone SS4036	|		|	scientific name	|
+156779	|	Cyanophage clone SS4038	|		|	scientific name	|
+156780	|	Cyanophage clone SS4041	|		|	scientific name	|
+156781	|	Cyanophage clone SS4042	|		|	scientific name	|
+156782	|	Cyanophage clone SS4046	|		|	scientific name	|
+156783	|	Cyanophage clone SS4051	|		|	scientific name	|
+156784	|	Cyanophage clone SS4055	|		|	scientific name	|
+156785	|	Cyanophage clone SS4059	|		|	scientific name	|
+156786	|	Cyanophage clone SS4061	|		|	scientific name	|
+156787	|	Cyanophage clone SS4064	|		|	scientific name	|
+156788	|	Cyanophage clone SS4065	|		|	scientific name	|
+156789	|	Cyanophage clone SS4066	|		|	scientific name	|
+156790	|	Cyanophage clone SS4067	|		|	scientific name	|
+156791	|	Cyanophage clone SS4073	|		|	scientific name	|
+156792	|	Cyanophage clone SS4074	|		|	scientific name	|
+156797	|	Cyanophage clone SS4733	|		|	scientific name	|
+156798	|	Cyanophage clone SS4731	|		|	scientific name	|
+156799	|	Cyanophage clone SS4729	|		|	scientific name	|
+156800	|	Cyanophage clone SS4726	|		|	scientific name	|
+156801	|	Cyanophage clone SS4725	|		|	scientific name	|
+156802	|	Cyanophage clone SS4723	|		|	scientific name	|
+156803	|	Cyanophage clone SS4720	|		|	scientific name	|
+156804	|	Cyanophage clone SS4718	|		|	scientific name	|
+156805	|	Cyanophage clone SS4717	|		|	scientific name	|
+156806	|	Cyanophage clone SS4716	|		|	scientific name	|
+156807	|	Cyanophage clone SS4715	|		|	scientific name	|
+156808	|	Cyanophage clone SS4714	|		|	scientific name	|
+156809	|	Cyanophage clone SS4713	|		|	scientific name	|
+156810	|	Cyanophage clone SS4710	|		|	scientific name	|
+156811	|	Cyanophage clone SS4707	|		|	scientific name	|
+156812	|	Cyanophage clone SS4706	|		|	scientific name	|
+156813	|	Cyanophage clone SS4705	|		|	scientific name	|
+156814	|	Cyanophage clone SS4703	|		|	scientific name	|
+156815	|	Cyanophage clone SS4702	|		|	scientific name	|
+156816	|	Cyanophage clone SS4701	|		|	scientific name	|
+156817	|	Cyanophage clone SS4734	|		|	scientific name	|
+156818	|	Cyanophage clone SS4736	|		|	scientific name	|
+156819	|	Cyanophage clone SS4737	|		|	scientific name	|
+156820	|	Cyanophage clone SS4738	|		|	scientific name	|
+156821	|	Cyanophage clone SS4803	|		|	scientific name	|
+156822	|	Cyanophage clone SS4804	|		|	scientific name	|
+156823	|	Cyanophage clone SS4805	|		|	scientific name	|
+156824	|	Cyanophage clone SS4809	|		|	scientific name	|
+156825	|	Cyanophage clone SS4810	|		|	scientific name	|
+156826	|	Cyanophage clone SS4813	|		|	scientific name	|
+156827	|	Cyanophage clone SS4814	|		|	scientific name	|
+156828	|	Cyanophage clone SS4821	|		|	scientific name	|
+156829	|	Cyanophage clone SS4824	|		|	scientific name	|
+156830	|	Cyanophage clone SS4827	|		|	scientific name	|
+156831	|	Cyanophage clone SS4829	|		|	scientific name	|
+156832	|	Cyanophage clone SS4832	|		|	scientific name	|
+156833	|	Cyanophage clone SS4838	|		|	scientific name	|
+156834	|	Cyanophage clone SS4845	|		|	scientific name	|
+156835	|	Cyanophage clone SS4850	|		|	scientific name	|
+215796	|	uncultured cyanophage	|		|	scientific name	|
+278008	|	uncultured bacteriophage	|		|	synonym	|
+278008	|	uncultured phage	|		|	scientific name	|
+306552	|	uncultured aquatic bacteriophage	|		|	synonym	|
+306552	|	uncultured aquatic phage	|		|	scientific name	|
+432371	|	Halophage AAJ-2005	|		|	synonym	|
+432371	|	environmental halophage 1 AAJ-2005	|		|	scientific name	|
+436674	|	environmental halophage	|		|	scientific name	|
+445563	|	uncultured desert soil virus	|		|	scientific name	|
+445564	|	uncultured prairie soil virus	|		|	scientific name	|
+445565	|	uncultured rainforest soil virus	|		|	scientific name	|
+707152	|	uncultured marine phage	|		|	scientific name	|
+1168811	|	environmental Halophage eHP-1	|		|	scientific name	|
+1168812	|	environmental Halophage eHP-10	|		|	scientific name	|
+1168813	|	environmental Halophage eHP-11	|		|	scientific name	|
+1168814	|	environmental Halophage eHP-12	|		|	scientific name	|
+1168815	|	environmental Halophage eHP-13	|		|	scientific name	|
+1168816	|	environmental Halophage eHP-14	|		|	scientific name	|
+1168817	|	environmental Halophage eHP-15	|		|	scientific name	|
+1168818	|	environmental Halophage eHP-16	|		|	scientific name	|
+1168819	|	environmental Halophage eHP-17	|		|	scientific name	|
+1168820	|	environmental Halophage eHP-18	|		|	scientific name	|
+1168821	|	environmental Halophage eHP-19	|		|	scientific name	|
+1168822	|	environmental Halophage eHP-2	|		|	scientific name	|
+1168823	|	environmental Halophage eHP-20	|		|	scientific name	|
+1168824	|	environmental Halophage eHP-22	|		|	scientific name	|
+1168825	|	environmental Halophage eHP-23	|		|	scientific name	|
+1168826	|	environmental Halophage eHP-24	|		|	scientific name	|
+1168827	|	environmental Halophage eHP-25	|		|	scientific name	|
+1168828	|	environmental Halophage eHP-27	|		|	scientific name	|
+1168829	|	environmental Halophage eHP-28	|		|	scientific name	|
+1168830	|	environmental Halophage eHP-29	|		|	scientific name	|
+1168831	|	environmental Halophage eHP-3	|		|	scientific name	|
+1168832	|	environmental Halophage eHP-30	|		|	scientific name	|
+1168833	|	environmental Halophage eHP-31	|		|	scientific name	|
+1168834	|	environmental Halophage eHP-32	|		|	scientific name	|
+1168835	|	environmental Halophage eHP-33	|		|	scientific name	|
+1168836	|	environmental Halophage eHP-34	|		|	scientific name	|
+1168837	|	environmental Halophage eHP-35	|		|	scientific name	|
+1168838	|	environmental Halophage eHP-36	|		|	scientific name	|
+1168839	|	environmental Halophage eHP-37	|		|	scientific name	|
+1168840	|	environmental Halophage eHP-38	|		|	scientific name	|
+1168841	|	environmental Halophage eHP-39	|		|	scientific name	|
+1168842	|	environmental Halophage eHP-4	|		|	scientific name	|
+1168843	|	environmental Halophage eHP-40	|		|	scientific name	|
+1168844	|	environmental Halophage eHP-41	|		|	scientific name	|
+1168845	|	environmental Halophage eHP-42	|		|	scientific name	|
+1168846	|	environmental Halophage eHP-5	|		|	scientific name	|
+1168847	|	environmental Halophage eHP-6	|		|	scientific name	|
+1168848	|	environmental Halophage eHP-7	|		|	scientific name	|
+1168849	|	environmental Halophage eHP-8	|		|	scientific name	|
+1168850	|	environmental Halophage eHP-9	|		|	scientific name	|
+1168851	|	environmental Halophage eHP-D7	|		|	scientific name	|
+1168852	|	environmental Halophage eHP-E5	|		|	scientific name	|
+164125	|	Mycobacteriophage L1	|		|	synonym	|
+164125	|	Mycobacterium phage L1	|		|	scientific name	|
+167320	|	Actinophage Q5	|		|	scientific name	|
+167533	|	Bartonella quintana phage	|		|	scientific name	|
+172666	|	Bacteriophage 6220	|		|	synonym	|
+172666	|	Enterobacteria phage 6220	|		|	scientific name	|
+173830	|	Bacteriophage Lahn1	|		|	synonym	|
+173830	|	Enterobacteria phage Lahn1	|		|	scientific name	|
+173831	|	Bacteriophage Lahn3	|		|	synonym	|
+173831	|	Enterobacteria phage Lahn3	|		|	scientific name	|
+176100	|	Bacteriophage U153	|		|	synonym	|
+176100	|	Listeria phage U153	|		|	scientific name	|
+181120	|	Bacteriophage C1	|		|	synonym	|
+181120	|	C1 bacteriophage	|		|	synonym	|
+181120	|	Enterobacteria phage C-1	|		|	scientific name	|
+181485	|	Bacteriophage fOg44	|		|	synonym	|
+181485	|	Oenococcus oeni bacteriophage fOg44	|		|	synonym	|
+181485	|	Oenococcus oeni temperate bacteriophage fOg44	|		|	synonym	|
+181485	|	Oenococcus phage fOg44	|		|	scientific name	|
+185368	|	Lactococcus phage 409	|		|	scientific name	|
+185369	|	Lactococcus phage F7/2	|		|	scientific name	|
+187176	|	Escherichia coli K12 phage EH297	|		|	synonym	|
+187176	|	Escherichia coli phage EH297	|		|	scientific name	|
+196194	|	Lactobacillus helveticus phage f-0303	|		|	synonym	|
+196194	|	Lactobacillus phage f-0303	|		|	scientific name	|
+198932	|	Streptococcus canis phage phisc1	|		|	synonym	|
+198932	|	Streptococcus phage phisc1	|		|	scientific name	|
+210927	|	Bacteriophage SC370	|		|	synonym	|
+210927	|	Enterobacteria phage SC370	|		|	scientific name	|
+219292	|	Bacteriophage pMLP1	|		|	synonym	|
+219292	|	Micromonospora phage pMLP1	|		|	scientific name	|
+221993	|	Bacteriophage f237	|		|	synonym	|
+221993	|	Vibrio phage f237	|		|	scientific name	|
+229343	|	Bacillus anthracis phage lambda Ba01	|		|	synonym	|
+229343	|	Bacillus phage lambda Ba01	|		|	scientific name	|
+229344	|	Bacillus anthracis phage lambda Ba02	|		|	synonym	|
+229344	|	Bacillus phage lambda Ba02	|		|	scientific name	|
+229345	|	Bacillus anthracis phage lambda Ba03	|		|	synonym	|
+229345	|	Bacillus phage lambda Ba03	|		|	scientific name	|
+229346	|	Bacillus anthracis phage lambda Ba04	|		|	synonym	|
+229346	|	Bacillus phage lambda Ba04	|		|	scientific name	|
+239740	|	Hybrid phage HybP-Knphi	|		|	scientific name	|
+241652	|	Bacteriophage FIZ15	|		|	synonym	|
+241652	|	Enterobacteria phage FIZ15	|		|	scientific name	|
+242708	|	Bacteriophage HybRS-Knphi	|		|	synonym	|
+242708	|	Vibrio phage HybRS-Knphi	|		|	scientific name	|
+262790	|	Bacteriophage WOcauB1	|		|	synonym	|
+262790	|	Wolbachia phage WOcauB1	|		|	scientific name	|
+264484	|	Bacteriophage KPP95	|		|	synonym	|
+264484	|	Klebsiella phage KPP95	|		|	scientific name	|
+268585	|	Bacteriophage V11	|		|	synonym	|
+268585	|	Enterobacteria phage V11	|		|	scientific name	|
+268586	|	Bacteriophage C14	|		|	synonym	|
+268586	|	Enterobacteria phage C14	|		|	scientific name	|
+268587	|	Bacteriophage C1.2	|		|	synonym	|
+268587	|	Enterobacteria phage C1.2	|		|	scientific name	|
+268588	|	Bacteriophage L1	|		|	synonym	|
+268588	|	E. coli O157:H7-specific bacteriophage L1	|		|	synonym	|
+268588	|	Enterobacteria phage L1	|		|	scientific name	|
+268590	|	Bacteriophage Ly1	|		|	synonym	|
+268590	|	Enterobacteria phage Ly1	|		|	scientific name	|
+272473	|	Bacteriophage TS2126	|		|	synonym	|
+272473	|	Phage TS2126	|		|	scientific name	|
+272757	|	Lactobacillus gasseri bacteriophage phigaY	|		|	synonym	|
+272757	|	Lactobacillus phage phigaY	|		|	scientific name	|
+279276	|	Equine faecal bacteriophage	|		|	synonym	|
+279276	|	Equine faecal phage	|		|	scientific name	|
+280702	|	Bacteriophage phiMFV1	|		|	synonym	|
+280702	|	Mycoplasma phage phiMFV1	|		|	scientific name	|
+282372	|	Phage Gifsy-3	|		|	scientific name	|
+282372	|	Prophage Gifsy-3	|		|	acronym	|
+282372	|	Salmonella phage Gifsy-3	|		|	synonym	|
+282690	|	Bacteriophage A75	|		|	synonym	|
+282690	|	Enterobacteria phage A75	|		|	scientific name	|
+282691	|	Bacteriophage A534	|		|	synonym	|
+282691	|	Enterobacteria phage A534	|		|	scientific name	|
+282692	|	Bacteriophage A557	|		|	synonym	|
+282692	|	Enterobacteria phage A557	|		|	scientific name	|
+282693	|	Bacteriophage O157-572	|		|	synonym	|
+282693	|	Enterobacteria phage O157-572	|		|	scientific name	|
+282698	|	Bacteriophage A312	|		|	synonym	|
+282698	|	Enterobacteria phage A312	|		|	scientific name	|
+282699	|	Bacteriophage A315	|		|	synonym	|
+282699	|	Enterobacteria phage A315	|		|	scientific name	|
+282700	|	Bacteriophage A549	|		|	synonym	|
+282700	|	Enterobacteria phage A549	|		|	scientific name	|
+282701	|	Bacteriophage A580	|		|	synonym	|
+282701	|	Enterobacteria phage A580	|		|	scientific name	|
+282702	|	Bacteriophage O157-292	|		|	synonym	|
+282702	|	Enterobacteria phage O157-292	|		|	scientific name	|
+282703	|	Bacteriophage O157-330	|		|	synonym	|
+282703	|	Enterobacteria phage O157-330	|		|	scientific name	|
+282704	|	Bacteriophage O157-310	|		|	synonym	|
+282704	|	Enterobacteria phage O157-310	|		|	scientific name	|
+282705	|	Bacteriophage O157-379	|		|	synonym	|
+282705	|	Enterobacteria phage O157-379	|		|	scientific name	|
+282709	|	Bacteriophage A397	|		|	synonym	|
+282709	|	Enterobacteria phage A397	|		|	scientific name	|
+282710	|	Bacteriophage O157-469	|		|	synonym	|
+282710	|	Enterobacteria phage O157-469	|		|	scientific name	|
+284052	|	Bacteriophage phi WMY	|		|	synonym	|
+284052	|	Staphylococcus phage phiWMY	|		|	scientific name	|
+291401	|	Bacteriophage CP-1639	|		|	synonym	|
+291401	|	Enterobacteria phage CP-1639	|		|	scientific name	|
+291401	|	Prophage CP-1639	|		|	synonym	|
+292511	|	Lactobacillus delbrueckii phage MZ-2004	|		|	synonym	|
+292511	|	Lactobacillus delbrueckii subsp. lactis phage AI15	|		|	synonym	|
+292511	|	Lactobacillus phage AI15	|		|	scientific name	|
+293378	|	Streptococcus pyogenes phage phiRamid	|		|	scientific name	|
+293378	|	prophage Phi M1T1.Z	|		|	synonym	|
+293711	|	Streptococcus pyogenes phage 5005.1	|		|	scientific name	|
+293712	|	Streptococcus pyogenes phage 5005.2	|		|	scientific name	|
+293713	|	Streptococcus pyogenes phage 5005.3	|		|	scientific name	|
+294363	|	Bacteriophage 020324	|		|	synonym	|
+294363	|	Enterobacteria phage 020324	|		|	scientific name	|
+311221	|	Bacillus thuringiensis phage MZTP02	|		|	scientific name	|
+319711	|	Streptococcus pyogenes phage 6180.2	|		|	scientific name	|
+319712	|	Streptococcus pyogenes phage 6180.3	|		|	scientific name	|
+319713	|	Streptococcus pyogenes phage 6180.4	|		|	scientific name	|
+334523	|	Phage SK137	|		|	scientific name	|
+338345	|	Bacteriophage Nil3	|		|	synonym	|
+338345	|	Enterobacteria phage Nil3	|		|	scientific name	|
+347331	|	Bacteriophage PA16	|		|	synonym	|
+347331	|	Pseudomonas phage PA16	|		|	scientific name	|
+350104	|	Bacteriophage 700P1	|		|	synonym	|
+350104	|	Streptococcus phage 700P1	|		|	scientific name	|
+350104	|	Streptococcus uberis bacteriophage 700P1	|		|	synonym	|
+356350	|	Phage 258-320	|		|	scientific name	|
+357204	|	Bacteriophage PPA5	|		|	synonym	|
+357204	|	Pseudomonas phage PPA5	|		|	scientific name	|
+360048	|	Burkholderia phage 644-2	|		|	scientific name	|
+360048	|	Burkholderia pseudomallei phage 644-2	|		|	synonym	|
+360049	|	Burkholderia phage E12-2	|		|	scientific name	|
+360049	|	Burkholderia pseudomallei phage E12-2	|		|	synonym	|
+360050	|	Burkholderia phage E202	|		|	scientific name	|
+360050	|	Burkholderia thailandensis phage E202	|		|	synonym	|
+362866	|	Cyanophage AN-15	|		|	scientific name	|
+362866	|	Temperate cyanophage AN-15	|		|	synonym	|
+364251	|	Bacteriophage Sal2	|		|	synonym	|
+364251	|	Lactobacillus phage Sal2	|		|	scientific name	|
+364252	|	Bacteriophage Sal1	|		|	synonym	|
+364252	|	Lactobacillus phage Sal1	|		|	scientific name	|
+364253	|	Bacteriophage Sal4	|		|	synonym	|
+364253	|	Lactobacillus phage Sal4	|		|	scientific name	|
+364254	|	Bacteriophage Sal3	|		|	synonym	|
+364254	|	Lactobacillus phage Sal3	|		|	scientific name	|
+370564	|	Bacteriophage 2096.1	|		|	synonym	|
+370564	|	Streptococcus phage 2096.1	|		|	scientific name	|
+370565	|	Bacteriophage 2096.2	|		|	synonym	|
+370565	|	Streptococcus phage 2096.2	|		|	scientific name	|
+374421	|	Bacteriophage phiK38-1	|		|	synonym	|
+374421	|	Streptomyces phage phiK38-1	|		|	scientific name	|
+375032	|	Synechococcus phage S	|		|	scientific name	|
+375033	|	Synechococcus phage S-IO9	|		|	scientific name	|
+375034	|	Synechococcus phage S-IO10	|		|	scientific name	|
+375035	|	Synechococcus phage S-IO15	|		|	scientific name	|
+375036	|	Synechococcus phage S-IO16	|		|	scientific name	|
+375037	|	Synechococcus phage S-IO20	|		|	scientific name	|
+375038	|	Synechococcus phage S-IO23	|		|	scientific name	|
+375039	|	Synechococcus phage S-IO36	|		|	scientific name	|
+375040	|	Synechococcus phage S-IO37	|		|	scientific name	|
+375041	|	Synechococcus phage S-IO40	|		|	scientific name	|
+375042	|	Synechococcus phage S-IO41	|		|	scientific name	|
+375043	|	Synechococcus phage S-IO42	|		|	scientific name	|
+375044	|	Synechococcus phage S-IO43	|		|	scientific name	|
+375045	|	Synechococcus phage S-IO46	|		|	scientific name	|
+375046	|	Synechococcus phage S-IO11	|		|	scientific name	|
+375047	|	Synechococcus phage S-IO12	|		|	scientific name	|
+375048	|	Synechococcus phage S-IO13	|		|	scientific name	|
+375049	|	Synechococcus phage S-IO14	|		|	scientific name	|
+375050	|	Synechococcus phage S-IO17	|		|	scientific name	|
+375051	|	Synechococcus phage S-IO18	|		|	scientific name	|
+375052	|	Synechococcus phage S-IO21	|		|	scientific name	|
+375053	|	Synechococcus phage S-IO22	|		|	scientific name	|
+375054	|	Synechococcus phage S-IO25	|		|	scientific name	|
+375055	|	Synechococcus phage S-IO26	|		|	scientific name	|
+375056	|	Synechococcus phage S-IO27	|		|	scientific name	|
+375057	|	Synechococcus phage S-IO47	|		|	scientific name	|
+375058	|	Synechococcus phage S-IO7	|		|	scientific name	|
+375059	|	Synechococcus phage S-IO8	|		|	scientific name	|
+382277	|	Synechococcus cyanophage S-SM1	|		|	scientific name	|
+382278	|	Synechococcus cyanophage S-SSM1	|		|	scientific name	|
+382279	|	Synechococcus cyanophage S-SSM2	|		|	scientific name	|
+382280	|	Synechococcus cyanophage S-SSM3	|		|	scientific name	|
+382281	|	Synechococcus cyanophage S-SSM5	|		|	scientific name	|
+382282	|	Synechococcus cyanophage S-ShM1	|		|	scientific name	|
+382283	|	Synechococcus cyanophage S-ShM2	|		|	scientific name	|
+376611	|	Lactobacillus casei phage Lca1	|		|	scientific name	|
+382263	|	Prochlorococcus cyanophage P-RSM2	|		|	scientific name	|
+382264	|	Prochlorococcus cyanophage P-RSM3	|		|	scientific name	|
+382265	|	Prochlorococcus cyanophage P-RSM5	|		|	scientific name	|
+382266	|	Prochlorococcus cyanophage P-SSM1	|		|	scientific name	|
+382267	|	Prochlorococcus cyanophage P-SSM10	|		|	scientific name	|
+382268	|	Prochlorococcus cyanophage P-SSM12	|		|	scientific name	|
+382269	|	Prochlorococcus cyanophage P-SSM3	|		|	scientific name	|
+382271	|	Prochlorococcus cyanophage P-SSM8	|		|	scientific name	|
+382272	|	Prochlorococcus cyanophage P-SSM9	|		|	scientific name	|
+382274	|	Prochlorococcus cyanophage P-SSP5	|		|	scientific name	|
+387086	|	Bacteriophage 10750	|		|	synonym	|
+387086	|	Streptococcus pyogenes MGAS10750 phage	|		|	scientific name	|
+370566	|	Bacteriophage 10750.1	|		|	synonym	|
+370566	|	Streptococcus phage 10750.1	|		|	scientific name	|
+370567	|	Bacteriophage 10750.2	|		|	synonym	|
+370567	|	Streptococcus phage 10750.2	|		|	scientific name	|
+370568	|	Bacteriophage 10750.3	|		|	synonym	|
+370568	|	Streptococcus phage 10750.3	|		|	scientific name	|
+370569	|	Bacteriophage 10750.4	|		|	synonym	|
+370569	|	Streptococcus phage 10750.4	|		|	scientific name	|
+387087	|	Streptococcus pyogenes MGAS10270 phage	|		|	scientific name	|
+370559	|	Bacteriophage 10270.1	|		|	synonym	|
+370559	|	Streptococcus phage 10270.1	|		|	scientific name	|
+370560	|	Bacteriophage 10270.2	|		|	synonym	|
+370560	|	Streptococcus phage 10270.2	|		|	scientific name	|
+370561	|	Bacteriophage 10270.3	|		|	synonym	|
+370561	|	Streptococcus phage 10270.3	|		|	scientific name	|
+370562	|	Bacteriophage 10270.4	|		|	synonym	|
+370562	|	Streptococcus phage 10270.4	|		|	scientific name	|
+370563	|	Bacteriophage 10270.5	|		|	synonym	|
+370563	|	Streptococcus phage 10270.5	|		|	scientific name	|
+387088	|	Streptococcus pyogenes MGAS9429 phage	|		|	scientific name	|
+370556	|	Bacteriophage 9429.1	|		|	synonym	|
+370556	|	Streptococcus phage 9429.1	|		|	scientific name	|
+370557	|	Bacteriophage 9429.2	|		|	synonym	|
+370557	|	Streptococcus phage 9429.2	|		|	scientific name	|
+370558	|	Bacteriophage 9428.3	|		|	synonym	|
+370558	|	Streptococcus phage 9428.3	|		|	scientific name	|
+405001	|	Burkholderia phage E255	|		|	scientific name	|
+405001	|	Burkholderia pseudomallei phage E255	|		|	synonym	|
+405001	|	Burkholderia thailandensis phage E255	|		|	synonym	|
+409026	|	Bacteriophage Swp3	|		|	synonym	|
+409026	|	Phage Swp3	|		|	scientific name	|
+417289	|	Saccharopolyspora erythraea prophage pSE101	|		|	scientific name	|
+417290	|	Saccharopolyspora erythraea prophage pSE211	|		|	scientific name	|
+430512	|	Streptococcus phage 370.1	|		|	scientific name	|
+430513	|	Streptococcus phage 370.3	|		|	scientific name	|
+430514	|	Streptococcus phage 370.2	|		|	scientific name	|
+430515	|	Streptococcus phage 370.4	|		|	scientific name	|
+432197	|	Enterobacteria phage CL707	|		|	scientific name	|
+432199	|	Enterobacteria phage HK244	|		|	scientific name	|
+432202	|	Enterobacteria phage mEp234	|		|	scientific name	|
+432203	|	Enterobacteria phage mEp332	|		|	scientific name	|
+435305	|	Vibrio phage KA-2007	|		|	scientific name	|
+435637	|	Coliphage K1A	|		|	synonym	|
+435637	|	Enterobacteria phage K1A	|		|	scientific name	|
+440576	|	Leuconostoc phage L5	|		|	scientific name	|
+445701	|	Cyanophage M4-283	|		|	scientific name	|
+447796	|	Enterobacteria bacteriophage T5-D1	|		|	synonym	|
+447796	|	Enterobacteria phage T5-D1	|		|	scientific name	|
+447800	|	Enterobacteria phage T5-A1	|		|	scientific name	|
+449399	|	Klebsiella phage PhiKPN	|		|	scientific name	|
+458420	|	Novosphingobium phage N-AFCM0615-3	|		|	scientific name	|
+458421	|	Novosphingobium phage N-AFCa0615-4	|		|	scientific name	|
+458422	|	Novosphingobium phage N-AFCa0615-5	|		|	scientific name	|
+458423	|	Novosphingobium phage N-AFCa0615-6	|		|	scientific name	|
+458424	|	Novosphingobium phage N-AFNF0628-7	|		|	scientific name	|
+458425	|	Novosphingobium phage N-AFCF0628-8	|		|	scientific name	|
+458426	|	Novosphingobium phage N-AFCF0628-9	|		|	scientific name	|
+458427	|	Novosphingobium phage N-AFCa0628-10	|		|	scientific name	|
+458428	|	Novosphingobium phage N-AFCM0628-11	|		|	scientific name	|
+458429	|	Novosphingobium phage N-AFCa0628-12	|		|	scientific name	|
+458430	|	Novosphingobium phage N-AFNF0707-13	|		|	scientific name	|
+458431	|	Novosphingobium phage N-AFCF0707-14	|		|	scientific name	|
+458432	|	Novosphingobium phage N-AFCF0707-15	|		|	scientific name	|
+458433	|	Novosphingobium phage N-AFCF0707-16	|		|	scientific name	|
+458434	|	Novosphingobium phage N-AFCa0707-17	|		|	scientific name	|
+458435	|	Novosphingobium phage N-AFCa0707-18	|		|	scientific name	|
+458436	|	Novosphingobium phage N-AFNF0802-19	|		|	scientific name	|
+458437	|	Novosphingobium phage N-AFNF0802-20	|		|	scientific name	|
+458438	|	Novosphingobium phage N-AFCF0802-21	|		|	scientific name	|
+458439	|	Novosphingobium phage N-AFCF0802-22	|		|	scientific name	|
+458440	|	Novosphingobium phage N-AFCa0802-56	|		|	scientific name	|
+458441	|	Novosphingobium phage N-AFCa0802-23	|		|	scientific name	|
+458442	|	Novosphingobium phage N-AFCa0802-57	|		|	scientific name	|
+458443	|	Novosphingobium phage N-AFCa0802-24	|		|	scientific name	|
+458444	|	Novosphingobium phage N-AFNF0810-25	|		|	scientific name	|
+458445	|	Novosphingobium phage N-AFCF0810-26	|		|	scientific name	|
+458446	|	Novosphingobium phage N-AFCM0810-27	|		|	scientific name	|
+458447	|	Novosphingobium phage N-AFCM0810-28	|		|	scientific name	|
+458448	|	Novosphingobium phage N-AFCa0810-29	|		|	scientific name	|
+458449	|	Novosphingobium phage N-AFCa0810-30	|		|	scientific name	|
+458450	|	Novosphingobium phage N-AFNF0824-31	|		|	scientific name	|
+458451	|	Novosphingobium phage N-AFCF0824-32	|		|	scientific name	|
+458452	|	Novosphingobium phage N-AFCM0824-33	|		|	scientific name	|
+458453	|	Novosphingobium phage N-AFCa0824-34	|		|	scientific name	|
+458454	|	Novosphingobium phage N-AFCa0824-35	|		|	scientific name	|
+458455	|	Novosphingobium phage N-AFCa0824-36	|		|	scientific name	|
+458456	|	Novosphingobium phage N-AFCF0901-37	|		|	scientific name	|
+458457	|	Novosphingobium phage N-AFCM0901-40	|		|	scientific name	|
+458458	|	Novosphingobium phage N-AFCa0901-41	|		|	scientific name	|
+458459	|	Novosphingobium phage N-AFCa0901-42	|		|	scientific name	|
+458460	|	Novosphingobium phage N-AFNF0913-43	|		|	scientific name	|
+458461	|	Novosphingobium phage N-AFCM0913-47	|		|	scientific name	|
+458462	|	Novosphingobium phage N-AFCF0714-51	|		|	scientific name	|
+458463	|	Novosphingobium phage N-AFCM0714-52	|		|	scientific name	|
+458464	|	Novosphingobium phage N-AFNF0922-55	|		|	scientific name	|
+458465	|	Sphingomonas phage S-AFNF0615-61	|		|	scientific name	|
+458466	|	Sphingomonas phage S-AFCF0802-69	|		|	scientific name	|
+458467	|	Sphingomonas phage S-AFNF0810-70	|		|	scientific name	|
+458468	|	Sphingomonas phage S-AFCa0824-71	|		|	scientific name	|
+458469	|	Sphingomonas phage S-AFCa0901-72	|		|	scientific name	|
+458470	|	Novosphingobium phage N-AFCa0707-83	|		|	scientific name	|
+458471	|	Novosphingobium phage N-AFCa0714-84	|		|	scientific name	|
+458472	|	Novosphingobium phage N-AFCa0802-85	|		|	scientific name	|
+458473	|	Novosphingobium phage N-AFCM0802-86	|		|	scientific name	|
+458474	|	Novosphingobium phage N-AFCF0901-89	|		|	scientific name	|
+458475	|	Novosphingobium phage N-AFCa0901-90	|		|	scientific name	|
+458476	|	Novosphingobium phage N-AFCM0901-91	|		|	scientific name	|
+458477	|	Novosphingobium phage N-An-FWCa0913-92	|		|	scientific name	|
+462299	|	Enterobacteria phage VT1-Sakai	|		|	scientific name	|
+464033	|	Campylobacter phage CGC-2007	|		|	scientific name	|
+472964	|	Streptococcus phage NZ131.1	|		|	scientific name	|
+472965	|	Streptococcus phage NZ131.2	|		|	scientific name	|
+472966	|	Streptococcus phage NZ131.3	|		|	scientific name	|
+483783	|	Bacillus phage bg1	|		|	scientific name	|
+483784	|	Bacillus phage bg2	|		|	scientific name	|
+483785	|	Bacillus phage bg3	|		|	scientific name	|
+498338	|	Synechococcus phage SPGM99-02	|		|	scientific name	|
+498339	|	Synechococcus phage SPGM99-07	|		|	scientific name	|
+498340	|	Synechococcus phage SPGM99-10	|		|	scientific name	|
+498341	|	Synechococcus phage SPGM99-12	|		|	scientific name	|
+498342	|	Synechococcus phage SPGM99-14	|		|	scientific name	|
+498343	|	Synechococcus phage SPGM99-15	|		|	scientific name	|
+498344	|	Synechococcus phage SPGM99-16	|		|	scientific name	|
+498345	|	Synechococcus phage SPGM99-20	|		|	scientific name	|
+498346	|	Synechococcus phage SPGM99-21	|		|	scientific name	|
+498347	|	Synechococcus phage SPGM99-24	|		|	scientific name	|
+498348	|	Synechococcus phage SPGM99-27	|		|	scientific name	|
+498349	|	Synechococcus phage SPGM99-28	|		|	scientific name	|
+498350	|	Synechococcus phage SPGM99-29	|		|	scientific name	|
+498351	|	Synechococcus phage SPGM99-30	|		|	scientific name	|
+498352	|	Synechococcus phage SPGM99-31	|		|	scientific name	|
+498353	|	Synechococcus phage SPGM99-39	|		|	scientific name	|
+504556	|	Propionibacterium phage PAS7	|		|	scientific name	|
diff -r 000000000000 -r 7a76cd412252 test-data/taxdb/nodes.dmp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxdb/nodes.dmp	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,502 @@
+1	|	1	|	no rank	|		|	8	|	0	|	1	|	0	|	0	|	0	|	0	|	0	|		|
+10239	|	1	|	superkingdom	|		|	9	|	0	|	1	|	0	|	0	|	0	|	0	|	0	|		|
+12333	|	10239	|	no rank	|		|	3	|	0	|	11	|	0	|	0	|	1	|	0	|	0	|		|
+12340	|	12333	|	species	|	EP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12347	|	12333	|	species	|	AJ	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12366	|	12333	|	species	|	SP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12371	|	12333	|	species	|	PH	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12374	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12375	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12386	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12388	|	12333	|	species	|	MP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12392	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12403	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12404	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12405	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12406	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12408	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12409	|	12333	|	species	|	CP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12412	|	12333	|	species	|	SP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12413	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12420	|	12333	|	species	|	FP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12424	|	12333	|	species	|	PX	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12425	|	12333	|	species	|	PX	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12427	|	12333	|	species	|	LL	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+12428	|	12333	|	species	|	RP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+28368	|	12333	|	species	|	CD	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+31760	|	12333	|	species	|	CP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+33768	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+33769	|	12333	|	species	|	LP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+38018	|	12333	|	species	|	UP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+39425	|	12333	|	species	|	SP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+39943	|	12333	|	species	|	AJ	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+41669	|	12333	|	species	|	PL	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+42171	|	12333	|	species	|	PN	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+42172	|	12333	|	species	|	PX	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+42173	|	12333	|	species	|	PC	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+45331	|	12333	|	species	|	PF	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+45332	|	12333	|	species	|	PP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+45441	|	12333	|	species	|	EP	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
+48224	|	12333	|	species	|	PE	|	3	|	1	|	11	|	1	|	0	|	1	|	1	|	0	|		|
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diff -r 000000000000 -r 7a76cd412252 tool-data/ncbi_taxonomy.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ncbi_taxonomy.loc.sample	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,5 @@
+# Tab separated fields where
+# value is unique key
+# name is descriptive name
+# path is path to directory containing names.dmp and nodes.dmp files
+#value	name		path
diff -r 000000000000 -r 7a76cd412252 tool-data/ncbi_taxonomy_sqlite.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ncbi_taxonomy_sqlite.loc	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,1 @@
+test	test database	/tmp/tmpvD64FQ/tmpIn01Xk/tmpcfHY_f/database/data_manager_tool-dataP323iD/ncbi_taxonomy_sqlite/test
diff -r 000000000000 -r 7a76cd412252 tool-data/ncbi_taxonomy_sqlite.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ncbi_taxonomy_sqlite.loc.sample	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,2 @@
+#This file describes the storage location for the NCBI Taxonomy SQLite database file
+#<unique_name>      <description>  <file_path>
\ No newline at end of file
diff -r 000000000000 -r 7a76cd412252 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of taxonomy data downloaded from NCBI -->
+    <table name="ncbi_taxonomy" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/ncbi_taxonomy.loc" />
+    </table>
+    <!-- Locations of SQLite format NCBI Taxonomy database -->
+    <table name="ncbi_taxonomy_sqlite" comment_char="#">
+        <columns>value, description, path</columns>
+        <file path="tool-data/ncbi_taxonomy_sqlite.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 7a76cd412252 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Jul 21 17:04:41 2020 -0400
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of taxonomy data downloaded from NCBI -->
+    <table name="ncbi_taxonomy" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" />
+    </table>
+    <!-- Locations of SQLite format NCBI Taxonomy database -->
+    <table name="ncbi_taxonomy_sqlite" comment_char="#">
+        <columns>value, description, path</columns>
+        <file path="${__HERE__}/test-data/ncbi_taxonomy_sqlite.loc" />
+    </table>
+</tables>